Computational Molecular Physics WiSe 22/23
Description
This course discusses modern methods for simulations of molecular systems, with examples and applications.
Requirements:
The first part of the course is also offered within the module „Molecular simulation I“ of the Master’s program in Computational Sciences.
32 lectures (30 + exam week)
Monday 12-14 0.1.01 Hörsaal B - Arnimallee 14
Wednesday 12-14 0.1.01 Hörsaal B - Arnimallee 14
Tutorials: Tuesday 10-12 1.3.01 PC-Pool - Arnimallee 14
First day of lectures: October 17, 2022
Last day of lectures: February 15, 2022
First tutorial: October 25, 2022
Last tutorial: February 14, 2022
Winter break: December 17, 2022 – January 1, 2023
Course Chat:
https://matrix.to/#/!wHYOaQBanpDRoygcGj:physik.fu-berlin.de?via=physik.fu-berlin.de
You need an account in Physics to be able to join the chat. Please ask zedat to give you an account in Physics if you don't have one already.
Topics/Lectures:
(the schedule may be adjusted during the semester)
Oct 17 01. Introduction
Oct 19 02. Statistical Mechanics refresher
Oct 18 – No Tutorial
Oct 24 03. Statistical Mechanics refresher
Oct 26 04. From Statistical Mechanics to Molecular Dynamics
Oct 25 – Tutorial 01. Python primer
Oct 31 05. Molecular Dynamics: force-fields
Nov 2 06. Molecular Dynamics: integrators
Nov 1 – Tutorial 02. Python primer – hw 1 due
Nov 7 07. Molecular Dynamics: integrators
Nov 9 08. Molecular Dynamics: electrostatic treatment
Nov 8 – Introduction to MDtraj – hw 2 due
Nov 14 09. Molecular Dynamics: electrostatic treatment
Nov 16 10. Molecular Dynamics: electrostatic treatment
Nov 15 – Write your own integrator – hw 3 due
Nov 21 11. Molecular Dynamics: implicit & explicit solvent methods
Nov 23 12. Molecular Dynamics: simulations in different ensembles
Nov 22 – Write your own integrator – hw 4 due
Nov 28 13. Molecular Dynamics: simulations in different ensembles
Nov 30 14. Molecular Dynamics: Langevin Dynamics
Nov 29 – Use OpenMM – hw 5 due
Dec 5 15. Molecular Dynamics: Langevin Dynamics
Dec 7 16. Molecular Dynamics: equilibrium data analysis
Dec 6 – Use OpenMM – hw 6 due
Dec 12 17. Molecular Dynamics: equilibrium data analysis
Dec 14 18. Molecular Dynamics: kinetics & MSM
Dec 13 – Introduction to PyEmma – hw 7 due
Jan 2 19. Molecular Dynamics: kinetics & MSM
Jan 4 20. Molecular Dynamics: Enhanced Sampling and Adaptive Sampling
Jan 3 – Introduction to PyEmma – hw 8 due
Jan 9 21. Molecular Dynamics: Free Energy perturbation
Jan 11 22. Molecular Dynamics: coarse-graining
Jan 10 – Coarse-graining – hw 9 due
Jan 16 23. Molecular Dynamics: coarse-graining
Jan 18 24. Molecular Dynamics: machine-learning methods
Jan 17 – Normal Mode Analysis – hw 10 due
Jan 23 25. Molecular Dynamics: machine-learning methods
Jan 25 26. Finding minima and transition states in Free Energy Landscapes
Jan 24 – Monte Carlo – hw 11 due
Jan 30 27. Normal Mode Analysis
Feb 1 28. Monte Carlo simulations
Jan 31 – Summary/Preparation for exam
Feb 6 29. Markov Chain Monte Carlo
Feb 8 30. Parallel Tempering
Feb 7 – Summary/Preparation for exam
Feb 13 29. Exam week
Feb 15 30. Exam week
Feb 14 – Summary/Preparation for exam
| Course No | Course Type | Hours |
|---|---|---|
| 20122901 | Vorlesung | 4 |
| 20122902 | Übung | 2 |
| Time Span | 17.10.2022 - 15.02.2023 |
|---|---|
| Instructors |
Cecilia Clementi
|
| 0352c_MA120 | 2020, MSc Physik (Mono), 120 LP |
| 0496a_MA120 | 2016, MSc Computational Science (Mono), 120 LPs |
| Day | Time | Location | Details |
|---|---|---|---|
| Monday | 12-14 | 0.1.01 Hörsaal B | 2022-10-17 - 2023-02-13 |
| Wednesday | 12-14 | 0.1.01 Hörsaal B | 2022-10-19 - 2023-02-15 |
| Day | Time | Location | Details |
|---|---|---|---|
| Tuesday | 10-12 | Online | Iryna Zaporozhets |
IMPORTANT: MESSAGE FROM IRYNA ABOUT THE SOFTWARE YOU NEED FOR THE TUTORIAL
Dear Students!
Below is the list of software we need for this class and corresponding installation instructions. All the software in this course is free for academic and research purposes and is available for Linux, macOS, and Windows. Please, install everything before the tutorial on your laptop and bring it with you to the class. If you have any problems, questions, or concerns, please, contact me (via email at iryna.zaporozhets@fu-berlin.de or the Element server) or Prof. Clementi.
Looking forward to seeing you in the tutorials.
Best,
Iryna
SOFTWARE LIST
1) python with a set of python packages
The tutorial is python-based, and we will use many different python packages. To manage the packages and minimize the number of issues due to different package versions and dependency conflicts, I strongly recommend using Miniconda. You can download it here: https://docs.conda.io/en/latest/miniconda.html
Installation instructions:
https://conda.io/projects/conda/en/latest/user-guide/install/index.html
Once you have installed the Miniconda, follow the steps below to create an environment with all the packages we need.
1.1) Run the following commands:
conda create --name CMP -c conda-forge python=3.9 pyemma_tutorials openmm pdbfixer autopep8
This command will create an environment named CMP with python 3.9 and all the packages we need. You can replace CMP with any other environment name.
1.2) Once installation is complete (it will take some time), activate your environment by running
conda activate CMP
1.3) Check if you can successfully run the following command:
python -m openmm.testInstallation
1.4) Check if you can successfully run the following command:
jupyter notebook
Please, let me know if you encounter any problems or would like to organize packages differently (e. g., with pip ore venv).
2) git
Git is a version control system, and you can find the installation instructions here: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
When git is used in combination with some repository hosting service, for example, GitHub, it greatly simplifies collaboration and code sharing. I suggest you register at https://github.com/. Once you have an account, let me know your username so I can give you access to the class repository. Github is a commercial service (though free for you to use), so registration is not a requirement for the class, but it is a standard tool, and it would be good to learn how to use it.
3) VMD
VMD is software for molecular visualization that will allow us to explore biomolecules in 3D We will use the latest stable version of VMD, 1.9.3. You can find it here: (download is available after free registration): https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/
The installation instructions:
https://www.ks.uiuc.edu/Research/vmd/current/ig.pdf